A variance component-based gene burden test

Juan M. Peralta, Marcio Almeida, Jack W. Kent, John Blangero

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

We propose a novel variance component approach for the analysis of next-generation sequencing data. Our method is based on the detection of the proportion of the trait phenotypic variance that can be explained by the introduction of a new variance component that accounts for the local gene-specific departure of the empirical kinship relationship matrix, estimated from single-nucleotide polymorphism (SNP) genotypes, from their theoretical expectation based on the genealogical information in the pedigree. We tested our method with simulated phenotypes and imputed SNP genotypes from the Genetic Analysis Workshop 18 data set. We observed considerable variation in the differences between theoretical and gene-specific kinship estimates that proved to be informative for our test and allowed us to detect the MAP4 causal gene at a genome-wide significance level. The distribution of our test statistic show no inflation under the null hypothesis and results from a random set of genes suggest that the detection of MAP4 is both sensitive and specific. The use of 2 different strategies for the selection of the SNPs used to derive the gene-specific empirical kinship relationship matrices provides us with suggestive evidence that our method is performing as an empirical test of linkage.

Original languageEnglish (US)
Article numberS49
JournalBMC Proceedings
Volume8
DOIs
StatePublished - Jun 17 2014
Externally publishedYes

Fingerprint

Gene Components
Genes
Single Nucleotide Polymorphism
Polymorphism
Genotype
Nucleotides
Economic Inflation
Pedigree
Genome
Phenotype
Education
Statistics

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Peralta, J. M., Almeida, M., Kent, J. W., & Blangero, J. (2014). A variance component-based gene burden test. BMC Proceedings, 8, [S49]. https://doi.org/10.1186/1753-6561-8-S1-S49

A variance component-based gene burden test. / Peralta, Juan M.; Almeida, Marcio; Kent, Jack W.; Blangero, John.

In: BMC Proceedings, Vol. 8, S49, 17.06.2014.

Research output: Contribution to journalArticle

Peralta, JM, Almeida, M, Kent, JW & Blangero, J 2014, 'A variance component-based gene burden test', BMC Proceedings, vol. 8, S49. https://doi.org/10.1186/1753-6561-8-S1-S49
Peralta JM, Almeida M, Kent JW, Blangero J. A variance component-based gene burden test. BMC Proceedings. 2014 Jun 17;8. S49. https://doi.org/10.1186/1753-6561-8-S1-S49
Peralta, Juan M. ; Almeida, Marcio ; Kent, Jack W. ; Blangero, John. / A variance component-based gene burden test. In: BMC Proceedings. 2014 ; Vol. 8.
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